rs10993081

chr9-94177436-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_160773.1(LINC02603):n.551T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,290 control chromosomes in the GnomAD database, including 513 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.063 (513 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02603 NR_160773.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

LINC02603 (HGNC:37186): (long intergenic non-protein coding RNA 2603)

MIRLET7A1HG (HGNC:53970): (miRlet-7a-1/let-7f-1/let-7d cluster host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02603	NR_160773.1	n.551T>C		non_coding_transcript_exon_variant	3/3
MIRLET7A1HG	NR_170278.1	n.225+1471A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02603	ENST00000668497.1	n.701T>C		non_coding_transcript_exon_variant	3/3
MIRLET7A1HG	ENST00000710611.1	n.209+1471A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9667 AN: 152172 Hom.: 517 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0737

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 AFR exome AF: 0.00

GnomAD4 genome AF: 0.0634 AC: 9653 AN: 152290 Hom.: 513 Cov.: 33 AF XY: 0.0657 AC XY: 4895 AN XY: 74462

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.0986

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0623

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0710 Hom.: 792

Bravo AF: 0.0706

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.1
Dann	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10993081; hg19: chr9-96939718;